Research Highlight

The CCDB Releases a New Version of Web Site to Make Sharing Microscopy Data Easier.

Screenshots of the Cell Centered Database, 2007.

May 2007 — Originally deployed in March 2002 under the auspices of NIH’s Human Brain Project, the Cell Centered Database (CCDB) accommodates the storage and manipulation of high-resolution 3D light and electron microscopic reconstructions and facilitates advanced electron tomography. Today, the CCDB has grown into a federated database of linked multiscale biological knowledge that is an integral part of the Biomedical Informatics Research Network, a larger NIH initiative to foster large-scale biomedical science collaborations using high-speed networks and distributed software and data integration capabilities. Other features new to this release of the CCDB include an improved interface for easier searching and browsing capabilities, added movie storage functionality, a convenient dictionary of CCDB terms, and the addition of a Subcellular Anatomy Ontology (SAO) to facilitate the annotation and subsequent mining of images.

The CCDB is participating in several large scale information projects to develop and utilize ontologies and spatial reference systems for data mining and data federation. The CCDB’s incorporated of a new ontology for describing the subcellular neuroanatomy of neurons and glia and how these parts come together to define supracellular structures such as synapses and neuropil.

"The Ontology for Subcellular Anatomy of the Nervous System (SAO) is a significant step towards the use of ontologies to link data across scales and modalities. By providing a means to annotate cellular and subcellular data obtained from light and electron microscopy, researchers will be able to amass and integrate biological data across dimensional scales," explains Maryann Martone. "The SAO will promote data integration both by providing a common terminology for data annotation and the means by which relationships among diverse data can be inferred."

CCDB’s new image gallery enables users to upload and share movies and animations of cellular and subcellular structures. New animations recently added to the site include a set of surface rendered neurons from the cortex of patients with Alzheimer’s disease, generated through serial section electron microscopy. Subcellular organelles and pathological features such as paired helical filaments can be visually delineated in neurons exhibiting different degrees of pathology.

"The Cell Centered Database is different from most other image repositories because it was designed to accommodate detailed experimental metadata as well as images, so that researchers can readily review and share full 2D, 3D, and 4D datasets," says Maryann Martone, the principal architect of the project. Martone adds, "For example, the CCDB enables researchers to model the entire process of electron tomographic reconstruction, from specimen preparation to segmentation and analysis. Since proper interpretation of imaging data requires a thorough understanding of the experimental and imaging conditions used to produce the specimen and image, we’ve designed the CCDB to allow researchers to preserve parameters that we know are important for interpreting structural and protein distribution data."

The Cell Centered Database stores and manages cell level information from tissue, cultured cells, and subcellular fractions, regardless of the type of tissue being studied. Because a significant portion of the tomographic work performed at the NCMIR concerns such neuronal structures, the CCDB has several specializations specific for neuronal data. For example, the CCDB can link morphological metadata about the structure of individual nerve cells filled with fluorescent intracellular dyes to a series of optical slices, and other related data such as branching tree structures obtained using advanced software packages such as Neurolucida (MicroBrightField Inc.).

The CCDB provides researchers with a convenient way to link their microscopy data products and associated metadata with scholarly publications. For example, Moisan et al. (2006) deposited tomograms with complete experimental data and referenced the CCDB link as supplementary data in their journal article. In contrast to restrictions on the size of supplementary data permitted by many scholarly journals, the CCDB was designed to encourage researchers to archive and browse very large multi-dimensional datasets. For example, in order to share large-scale brain mosaics with the public, Diana Price and colleagues deposited a massive supplemental dataset into the CCDB (CCDB record ID 102103a) for online viewing and analysis (click to browse a coronal slice of anterior mouse hippocampus) and referenced the link in their scholarly publication (Price et al. 2006). In this way, the online brain maps provide a persistent digital archive of potentially valuable specimens to the public.

The CCDB team encourages microscopists and tomographers to consider the benefits of depositing their high quality datasets into this secure database. CCDB images and data may be freely downloaded and reused.

Citations

Moisan TA, MH Ellisman, CW Buitenhuys and GA Sosinsky (2006) Differences in chloroplast ultrastructure of Phaeocystis antarctica in low and high light. Marine Biology 149(6):1281-1290.

Price DL, Chow SK, MacLean NAB, Hakozaki H, Peltier S, Martone ME, Ellisman MH (2006) High-Resolution Large-Scale Mosaic Imaging using Multiphoton Microscopy to Characterize Transgenic Mouse Models of Human Neurological Disorders. Neuroinformatics 4(1):65-80.